Mercurial > repos > iuc > plink
comparison plink.xml @ 9:272aca44b3dd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
author | iuc |
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date | Sun, 19 Dec 2021 15:53:35 +0000 |
parents | 16d22eee0fe3 |
children | 2c0ac05fe240 |
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8:16d22eee0fe3 | 9:272aca44b3dd |
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1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> | 1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> |
2 <macros> | 2 <macros> |
3 <token name='@TOOL_VERSION@'>1.9.b618</token> | 3 <token name='@TOOL_VERSION@'>1.90b6.21</token> |
4 <token name='@VERSION_SUFFIX@'>3</token> | 4 <token name='@VERSION_SUFFIX@'>0</token> |
5 <xml name='template_sanitizer'> | 5 <xml name='template_sanitizer'> |
6 <sanitizer> | 6 <sanitizer> |
7 <valid initial='default'> | 7 <valid initial='default'> |
8 <add value='#' /> | 8 <add value='#' /> |
9 <add value='@' /> | 9 <add value='@' /> |
35 <valid initial='string.ascii_letters + string.digits'> | 35 <valid initial='string.ascii_letters + string.digits'> |
36 <add value=' '/> | 36 <add value=' '/> |
37 </valid> | 37 </valid> |
38 </sanitizer> | 38 </sanitizer> |
39 </xml> | 39 </xml> |
40 <xml name="log_out_assert"> | |
41 <output name="plink_log"> | |
42 <assert_contents> | |
43 <has_text text="End time:"/> | |
44 </assert_contents> | |
45 </output> | |
46 </xml> | |
40 </macros> | 47 </macros> |
41 <xrefs> | 48 <xrefs> |
42 <xref type="bio.tools">plink</xref> | 49 <xref type="bio.tools">plink</xref> |
43 </xrefs> | 50 </xrefs> |
44 <requirements> | 51 <requirements> |
45 <requirement type='package' version='1.90b6.18'>plink</requirement> | 52 <requirement type='package' version='@TOOL_VERSION@'>plink</requirement> |
46 </requirements> | 53 </requirements> |
47 <command detect_errors='exit_code'><![CDATA[ | 54 <command detect_errors='exit_code'><![CDATA[ |
48 | 55 |
49 ## Create Plink folder for any inputs | 56 ## Create Plink folder for any inputs |
50 mkdir ./plink_output | 57 mkdir ./plink_output |
53 | 60 |
54 ## If bmerge is set, create folder for merged files | 61 ## If bmerge is set, create folder for merged files |
55 #if $functions.func == 'data_manage': | 62 #if $functions.func == 'data_manage': |
56 #if $functions.bmerge.set == 'Yes': | 63 #if $functions.bmerge.set == 'Yes': |
57 && mkdir bmerge_files | 64 && mkdir bmerge_files |
58 && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed | 65 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bed bmerge_files/bmerge_input.bed |
59 && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim | 66 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bim bmerge_files/bmerge_input.bim |
60 && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam | 67 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.fam bmerge_files/bmerge_input.fam |
61 #end if | 68 #end if |
62 #end if | 69 #end if |
63 | 70 |
64 | 71 |
65 #if $inputs.inputs.filetype == 'bfile': | 72 #if $inputs.inputs.filetype == 'bfile': |
66 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed | 73 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bed plink_input/plink_input.bed |
67 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim | 74 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bim plink_input/plink_input.bim |
68 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam | 75 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.fam plink_input/plink_input.fam |
69 && plink --bfile plink_input/plink_input | 76 && plink --bfile plink_input/plink_input |
70 #elif $inputs.inputs.filetype == 'vcf': | 77 #elif $inputs.inputs.filetype == 'vcf': |
71 #if $inputs.inputs.input.is_of_type('bcf'): | 78 #if $inputs.inputs.input.is_of_type('bcf'): |
72 && plink --bcf '$inputs.inputs.input' | 79 && plink --bcf '$inputs.inputs.input' |
73 #else: | 80 #else: |
400 && mkdir assoc_out | 407 && mkdir assoc_out |
401 && mv ./plink_output/*asso* assoc_out | 408 && mv ./plink_output/*asso* assoc_out |
402 && find ./assoc_out/. -type f -exec mv {} {}.txt ';' | 409 && find ./assoc_out/. -type f -exec mv {} {}.txt ';' |
403 #end if | 410 #end if |
404 #end if | 411 #end if |
412 && mkdir '$plink_out.extra_files_path' | |
413 && cp plink_output/plink_output.bed '$plink_out.extra_files_path'/RgeneticsData.bed | |
414 && cp plink_output/plink_output.bim '$plink_out.extra_files_path'/RgeneticsData.bim | |
415 && cp plink_output/plink_output.fam '$plink_out.extra_files_path'/RgeneticsData.fam | |
405 ]]></command> | 416 ]]></command> |
406 <inputs> | 417 <inputs> |
407 <section name='inputs' title='Data inputs' expanded='true'> | 418 <section name='inputs' title='Data inputs' expanded='true'> |
408 <conditional name='inputs'> | 419 <conditional name='inputs'> |
409 <param name='filetype' type='select' label='Main input data type'> | 420 <param name='filetype' type='select' label='Main input data type'> |
410 <option value='bfile'>plink file</option> | 421 <option value='bfile'>plink file</option> |
411 <option value='vcf'>VCF input file</option> | 422 <option value='vcf'>VCF input file</option> |
412 </param> | 423 </param> |
413 <when value='bfile'> | 424 <when value='bfile'> |
414 <param format='pbed' name='bed' type='data' label='plink bed file'/> | 425 <param format='pbed' name='bed' type='data' label='plink bed file'/> |
415 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> | |
416 <param format='txt' name='fam' type='data' label='plink fam file'/> | |
417 </when> | 426 </when> |
418 <when value='vcf'> | 427 <when value='vcf'> |
419 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/> | 428 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/> |
420 </when> | 429 </when> |
421 </conditional> | 430 </conditional> |
669 <option value='No'>No</option> | 678 <option value='No'>No</option> |
670 <option value='Yes'>Yes</option> | 679 <option value='Yes'>Yes</option> |
671 </param> | 680 </param> |
672 <when value='No'/> | 681 <when value='No'/> |
673 <when value='Yes'> | 682 <when value='Yes'> |
674 <param format='binary' name='bed' type='data' label='plink bed file'/> | 683 <param format='pbed' name='bed' type='data' label='plink bed file'/> |
675 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> | |
676 <param format='tabular,tsv' name='fam' type='data' label='plink fam file'/> | |
677 </when> | 684 </when> |
678 </conditional> | 685 </conditional> |
679 <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/> | 686 <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/> |
680 <param format='tsv,tabular' name='flip' type='data' label='Flip DNA strand for SNPs' help='Given a file containing a list of SNPs with A/C/G/T alleles, --flip swaps A↔T and C↔G.' optional='true'/> | 687 <param format='tsv,tabular' name='flip' type='data' label='Flip DNA strand for SNPs' help='Given a file containing a list of SNPs with A/C/G/T alleles, --flip swaps A↔T and C↔G.' optional='true'/> |
681 <param name='template' type='text' label='Update Variant Info: Template String' help='Replaces missing IDs. The parameter taken by these flags is a special template string, with a @ where the chromosome code should go, and a # where the base-pair position belongs.'> | 688 <param name='template' type='text' label='Update Variant Info: Template String' help='Replaces missing IDs. The parameter taken by these flags is a special template string, with a @ where the chromosome code should go, and a # where the base-pair position belongs.'> |
800 <param name='window' type='integer' label='Window size in bp' value='50' help='Window size'/> | 807 <param name='window' type='integer' label='Window size in bp' value='50' help='Window size'/> |
801 <param name='step' type='integer' label='Step size (variant ct)' value='5'/> | 808 <param name='step' type='integer' label='Step size (variant ct)' value='5'/> |
802 <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' /> | 809 <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' /> |
803 </when> | 810 </when> |
804 </conditional> | 811 </conditional> |
805 | |
806 </when> | 812 </when> |
807 <when value='stratification'> | 813 <when value='stratification'> |
808 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/> | 814 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/> |
809 <conditional name='cluster'> | 815 <conditional name='cluster'> |
810 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'> | 816 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'> |
991 </when> --> | 997 </when> --> |
992 </conditional> | 998 </conditional> |
993 </inputs> | 999 </inputs> |
994 <outputs> | 1000 <outputs> |
995 <!--Main--> | 1001 <!--Main--> |
996 <collection name='plink_out' type='list' label='Plink main outputs'> | 1002 <data name="plink_out" format="pbed"/> |
997 <data name='plink_bed' format='pbed' from_work_dir='plink_output/plink_output.bed'/> | 1003 |
998 <data name='plink_bim' format='tabular' from_work_dir='plink_output/plink_output.bim'/> | 1004 <data name="plink_log" format='txt' from_work_dir='plink_output/plink_output.log' label='${tool.name} on ${on_string}: Log'/> |
999 <data name='plink_fam' format='txt' from_work_dir='plink_output/plink_output.fam'/> | |
1000 <data name='plink_log' format='txt' from_work_dir='plink_output/plink_output.log'/> | |
1001 </collection> | |
1002 | 1005 |
1003 <!--Data Manage--> | 1006 <!--Data Manage--> |
1004 <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name}: Recode ped'> | 1007 <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name} on ${on_string}: Recode ped'> |
1005 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> | 1008 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> |
1006 </data> | 1009 </data> |
1007 <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name}: Recode map'> | 1010 <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name} on ${on_string}: Recode map'> |
1008 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> | 1011 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> |
1009 </data> | 1012 </data> |
1010 | 1013 |
1011 <!--Stats--> | 1014 <!--Stats--> |
1012 <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name}: freq out'> | 1015 <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name} on ${on_string}: freq out'> |
1013 <filter>functions['func'] == 'stats' and functions['freq']</filter> | 1016 <filter>functions['func'] == 'stats' and functions['freq']</filter> |
1014 </data> | 1017 </data> |
1015 <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name}: Hardy-Weinberg equilibrium'> | 1018 <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name} on ${on_string}: Hardy-Weinberg equilibrium'> |
1016 <filter>functions['func'] == 'stats' and functions['hardy']</filter> | 1019 <filter>functions['func'] == 'stats' and functions['hardy']</filter> |
1017 </data> | 1020 </data> |
1018 <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name}: imiss'> | 1021 <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name} on ${on_string}: imiss'> |
1019 <filter>functions['func'] == 'stats' and functions['missing']</filter> | 1022 <filter>functions['func'] == 'stats' and functions['missing']</filter> |
1020 </data> | 1023 </data> |
1021 <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name}: lmiss'> | 1024 <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name} on ${on_string}: lmiss'> |
1022 <filter>functions['func'] == 'stats' and functions['missing']</filter> | 1025 <filter>functions['func'] == 'stats' and functions['missing']</filter> |
1023 </data> | 1026 </data> |
1024 <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name}: Het'> | 1027 <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name} on ${on_string}: Het'> |
1025 <filter>functions['func'] == 'stats' and functions['het']</filter> | 1028 <filter>functions['func'] == 'stats' and functions['het']</filter> |
1026 </data> | 1029 </data> |
1027 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'> | 1030 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name} on ${on_string}: Sex check'> |
1028 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter> | 1031 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter> |
1029 </data> | 1032 </data> |
1030 | 1033 |
1031 <!--Association--> | 1034 <!--Association--> |
1032 <!--Assoc --> | 1035 <!--Assoc --> |
1079 <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'> | 1082 <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'> |
1080 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes' and functions['cluster']['mds']['modifiers'] and 'eigvals' in functions['cluster']['mds']['modifiers']</filter> | 1083 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes' and functions['cluster']['mds']['modifiers'] and 'eigvals' in functions['cluster']['mds']['modifiers']</filter> |
1081 </data> | 1084 </data> |
1082 </outputs> | 1085 </outputs> |
1083 <tests> | 1086 <tests> |
1084 <test expect_num_outputs='5'> | 1087 <test expect_num_outputs='2'> |
1085 <section name='inputs'> | 1088 <section name='inputs'> |
1086 <conditional name='inputs'> | 1089 <conditional name='inputs'> |
1087 <param name='filetype' value='bfile'/> | 1090 <param name='filetype' value='bfile'/> |
1088 <param name='bed' value='plink.bed'/> | 1091 <param name='bed' value='' ftype="pbed"> |
1089 <param name='bim' value='plink.bim'/> | 1092 <composite_data value="plink.bim"/> |
1090 <param name='fam' value='plink.fam'/> | 1093 <composite_data value="plink.bed"/> |
1094 <composite_data value="plink.fam"/> | |
1095 </param> | |
1091 </conditional> | 1096 </conditional> |
1092 </section> | 1097 </section> |
1093 <conditional name='functions'> | 1098 <conditional name='functions'> |
1094 <param name='func' value='filtering'/> | 1099 <param name='func' value='filtering'/> |
1095 <conditional name='id_list'> | 1100 <conditional name='id_list'> |
1131 <param name='sex_select' value='--filter-cases'/> | 1136 <param name='sex_select' value='--filter-cases'/> |
1132 <param name='no_sex_select' value='--allow-no-sex'/> | 1137 <param name='no_sex_select' value='--allow-no-sex'/> |
1133 <param name='nonfounders' value='--nonfounders'/> | 1138 <param name='nonfounders' value='--nonfounders'/> |
1134 </conditional> | 1139 </conditional> |
1135 </conditional> | 1140 </conditional> |
1136 <output_collection name='plink_out' type='list'> | 1141 <output name="plink_out"> |
1137 <element name='plink_bed' file='test1_out.bed' compare='sim_size'/> | 1142 <extra_files type="file" name="RgeneticsData.bed" value="test1_out.bed" compare='sim_size'/> |
1138 <element name='plink_bim' file='test1_out.bim'/> | 1143 <extra_files type="file" name="RgeneticsData.bim" value="test1_out.bim"/> |
1139 <element name='plink_fam' file='test1_out.fam'/> | 1144 <extra_files type="file" name="RgeneticsData.fam" value="test1_out.fam"/> |
1140 </output_collection> | 1145 </output> |
1146 <expand macro="log_out_assert"/> | |
1141 </test> | 1147 </test> |
1142 | 1148 |
1143 <test expect_num_outputs='7'> | 1149 <test expect_num_outputs='4'> |
1144 <section name='inputs'> | 1150 <section name='inputs'> |
1145 <conditional name='inputs'> | 1151 <conditional name='inputs'> |
1146 <param name='filetype' value='bfile'/> | 1152 <param name='filetype' value='bfile'/> |
1147 <param name='bed' value='plink.bed'/> | 1153 <param name='bed' value='' ftype="pbed"> |
1148 <param name='bim' value='plink.bim'/> | 1154 <composite_data value="plink.bim"/> |
1149 <param name='fam' value='plink.fam'/> | 1155 <composite_data value="plink.bed"/> |
1156 <composite_data value="plink.fam"/> | |
1157 </param> | |
1150 </conditional> | 1158 </conditional> |
1151 </section> | 1159 </section> |
1152 <conditional name='functions'> | 1160 <conditional name='functions'> |
1153 <param name='func' value='data_manage'/> | 1161 <param name='func' value='data_manage'/> |
1154 <conditional name='bmerge'> | 1162 <conditional name='bmerge'> |
1155 <param name='set' value='Yes'/> | 1163 <param name='set' value='Yes'/> |
1156 <param name='bed' value='plink_2.bed'/> | 1164 <param name='bed' value='' ftype="pbed"> |
1157 <param name='bim' value='plink_2.bim'/> | 1165 <composite_data value="plink_2.bim"/> |
1158 <param name='fam' value='plink_2.fam'/> | 1166 <composite_data value="plink_2.bed"/> |
1167 <composite_data value="plink_2.fam"/> | |
1168 </param> | |
1159 </conditional> | 1169 </conditional> |
1160 <param name='recode' value='--recode'/> | 1170 <param name='recode' value='--recode'/> |
1161 <param name='template' value='@asd#123'/> | 1171 <param name='template' value='@asd#123'/> |
1162 <param name='length' value='23'/> | 1172 <param name='length' value='23'/> |
1163 <conditional name='update_cols'> | 1173 <conditional name='update_cols'> |
1166 <param name='col_num' value='1'/> | 1176 <param name='col_num' value='1'/> |
1167 <param name='var_col' value='2'/> | 1177 <param name='var_col' value='2'/> |
1168 <param name='skip' value='a'/> | 1178 <param name='skip' value='a'/> |
1169 </conditional> | 1179 </conditional> |
1170 </conditional> | 1180 </conditional> |
1171 <output_collection name='plink_out' type='list'> | 1181 <output name="plink_out"> |
1172 <element name='plink_bed' file='test2_out.bed' compare='sim_size'/> | 1182 <extra_files type="file" name="RgeneticsData.bed" value="test2_out.bed" compare='sim_size'/> |
1173 <element name='plink_bim' file='test2_out.bim'/> | 1183 <extra_files type="file" name="RgeneticsData.bim" value="test2_out.bim"/> |
1174 <element name='plink_fam' file='test2_out.fam'/> | 1184 <extra_files type="file" name="RgeneticsData.fam" value="test2_out.fam"/> |
1175 </output_collection> | 1185 </output> |
1186 <expand macro="log_out_assert"/> | |
1176 <output name='plink_ped' file='out.ped'/> | 1187 <output name='plink_ped' file='out.ped'/> |
1177 <output name='plink_map' file='out.map'/> | 1188 <output name='plink_map' file='out.map'/> |
1178 </test> | 1189 </test> |
1179 | 1190 |
1180 <test expect_num_outputs='5'> | 1191 <test expect_num_outputs='2'> |
1181 <section name='inputs'> | 1192 <section name='inputs'> |
1182 <conditional name='inputs'> | 1193 <conditional name='inputs'> |
1183 <param name='filetype' value='vcf'/> | 1194 <param name='filetype' value='vcf'/> |
1184 <param name='input' value='test.vcf'/> | 1195 <param name='input' value='test.vcf'/> |
1185 </conditional> | 1196 </conditional> |
1186 </section> | 1197 </section> |
1187 <output_collection name='plink_out' type='list'> | 1198 <output name="plink_out"> |
1188 <element name='plink_bed' file='vcf_out.bed'/> | 1199 <extra_files type="file" name="RgeneticsData.bed" value="vcf_out.bed" compare='sim_size'/> |
1189 <element name='plink_bim' file='vcf_out.bim'/> | 1200 <extra_files type="file" name="RgeneticsData.bim" value="vcf_out.bim"/> |
1190 <element name='plink_fam' file='vcf_out.fam'/> | 1201 <extra_files type="file" name="RgeneticsData.fam" value="vcf_out.fam"/> |
1191 </output_collection> | 1202 </output> |
1203 <expand macro="log_out_assert"/> | |
1192 </test> | 1204 </test> |
1193 | 1205 |
1194 <test expect_num_outputs='11'> | 1206 <test expect_num_outputs='8'> |
1195 <section name='inputs'> | 1207 <section name='inputs'> |
1196 <conditional name='inputs'> | 1208 <conditional name='inputs'> |
1197 <param name='filetype' value='bfile'/> | 1209 <param name='filetype' value='bfile'/> |
1198 <param name='bed' value='plink.bed'/> | 1210 <param name='bed' value='' ftype="pbed"> |
1199 <param name='bim' value='x_plink.bim'/> | 1211 <composite_data value="x_plink.bim"/> |
1200 <param name='fam' value='plink.fam'/> | 1212 <composite_data value="plink.bed"/> |
1213 <composite_data value="plink.fam"/> | |
1214 </param> | |
1201 </conditional> | 1215 </conditional> |
1202 </section> | 1216 </section> |
1203 <conditional name='functions'> | 1217 <conditional name='functions'> |
1204 <param name='func' value='stats'/> | 1218 <param name='func' value='stats'/> |
1205 <param name='freq' value='--freq'/> | 1219 <param name='freq' value='--freq'/> |
1215 <param name='female_max_obvs' value='10'/> | 1229 <param name='female_max_obvs' value='10'/> |
1216 <param name='male_min_obvs' value='200'/> | 1230 <param name='male_min_obvs' value='200'/> |
1217 </conditional> | 1231 </conditional> |
1218 </conditional> | 1232 </conditional> |
1219 </conditional> | 1233 </conditional> |
1220 <output_collection name='plink_out' type='list'> | 1234 <output name="plink_out"> |
1221 <element name='plink_bed' file='stats.bed'/> | 1235 <extra_files type="file" name="RgeneticsData.bed" value="stats.bed" compare='sim_size'/> |
1222 <element name='plink_bim' file='stats.bim'/> | 1236 <extra_files type="file" name="RgeneticsData.bim" value="stats.bim"/> |
1223 <element name='plink_fam' file='stats.fam'/> | 1237 <extra_files type="file" name="RgeneticsData.fam" value="stats.fam"/> |
1224 <element name='plink_fam' file='stats.fam'/> | 1238 </output> |
1225 </output_collection> | 1239 <expand macro="log_out_assert"/> |
1226 <output name='frequency' file='out.freq'/> | 1240 <output name='frequency' file='out.freq'/> |
1227 <output name='hardy_out' file='out.hardy'/> | 1241 <output name='hardy_out' file='out.hardy'/> |
1228 <output name='missing_1' file='out.imiss'/> | 1242 <output name='missing_1' file='out.imiss'/> |
1229 <output name='missing_2' file='out.lmiss'/> | 1243 <output name='missing_2' file='out.lmiss'/> |
1230 <output name='het' file='out.het'/> | 1244 <output name='het' file='out.het'/> |
1231 <output name='sex_check' file='out.sexcheck'/> | 1245 <output name='sex_check' file='out.sexcheck'/> |
1232 </test> | 1246 </test> |
1233 | 1247 |
1234 <test expect_num_outputs='7'> | 1248 <test expect_num_outputs='4'> |
1235 <section name='inputs'> | 1249 <section name='inputs'> |
1236 <conditional name='inputs'> | 1250 <conditional name='inputs'> |
1237 <param name='filetype' value='bfile'/> | 1251 <param name='filetype' value='bfile'/> |
1238 <param name='bed' value='plink.bed'/> | 1252 <param name='bed' value='' ftype="pbed"> |
1239 <param name='bim' value='plink.bim'/> | 1253 <composite_data value="plink.bim"/> |
1240 <param name='fam' value='plink.fam'/> | 1254 <composite_data value="plink.bed"/> |
1255 <composite_data value="plink.fam"/> | |
1256 </param> | |
1241 </conditional> | 1257 </conditional> |
1242 </section> | 1258 </section> |
1243 <conditional name='functions'> | 1259 <conditional name='functions'> |
1244 <param name='func' value='link'/> | 1260 <param name='func' value='link'/> |
1245 <conditional name='set_indep'> | 1261 <conditional name='set_indep'> |
1247 <param name='window' value='51'/> | 1263 <param name='window' value='51'/> |
1248 <param name='step' value='6'/> | 1264 <param name='step' value='6'/> |
1249 <param name='r2' value='0.3'/> | 1265 <param name='r2' value='0.3'/> |
1250 </conditional> | 1266 </conditional> |
1251 </conditional> | 1267 </conditional> |
1252 <output_collection name='plink_out' type='list'> | 1268 <output name="plink_out"> |
1253 <element name='plink_bed' file='test5_out.bed' compare='sim_size'/> | 1269 <extra_files type="file" name="RgeneticsData.bed" value="test5_out.bed" compare='sim_size'/> |
1254 <element name='plink_bim' file='test5_out.bim'/> | 1270 <extra_files type="file" name="RgeneticsData.bim" value="test5_out.bim"/> |
1255 <element name='plink_fam' file='test5_out.fam'/> | 1271 <extra_files type="file" name="RgeneticsData.fam" value="test5_out.fam"/> |
1256 </output_collection> | 1272 </output> |
1273 <expand macro="log_out_assert"/> | |
1257 <output name='prune_in' file='plink.prune.in'/> | 1274 <output name='prune_in' file='plink.prune.in'/> |
1258 </test> | 1275 </test> |
1259 | 1276 |
1260 <test expect_num_outputs='10'> | 1277 <test expect_num_outputs='7'> |
1261 <section name='inputs'> | 1278 <section name='inputs'> |
1262 <conditional name='inputs'> | 1279 <conditional name='inputs'> |
1263 <param name='filetype' value='bfile'/> | 1280 <param name='filetype' value='bfile'/> |
1264 <param name='bed' value='plink.bed'/> | 1281 <param name='bed' value='' ftype="pbed"> |
1265 <param name='bim' value='plink.bim'/> | 1282 <composite_data value="plink.bim"/> |
1266 <param name='fam' value='plink.fam'/> | 1283 <composite_data value="plink.bed"/> |
1284 <composite_data value="plink.fam"/> | |
1285 </param> | |
1267 </conditional> | 1286 </conditional> |
1268 </section> | 1287 </section> |
1269 <conditional name='functions'> | 1288 <conditional name='functions'> |
1270 <param name='func' value='stratification'/> | 1289 <param name='func' value='stratification'/> |
1271 <param name='read_genome' value='plink.genome'/> | 1290 <param name='read_genome' value='plink.genome'/> |
1277 <param name='dimensions' value='10'/> | 1296 <param name='dimensions' value='10'/> |
1278 <param name='modifiers' value='eigendecomp,eigvals'/> | 1297 <param name='modifiers' value='eigendecomp,eigvals'/> |
1279 </conditional> | 1298 </conditional> |
1280 </conditional> | 1299 </conditional> |
1281 </conditional> | 1300 </conditional> |
1282 <output_collection name='plink_out' type='list'> | 1301 <output name="plink_out"> |
1283 <element name='plink_bed' file='test6_out.bed' compare='sim_size'/> | 1302 <extra_files type="file" name="RgeneticsData.bed" value="test6_out.bed" compare='sim_size'/> |
1284 <element name='plink_bim' file='test6_out.bim'/> | 1303 <extra_files type="file" name="RgeneticsData.bim" value="test6_out.bim"/> |
1285 <element name='plink_fam' file='test6_out.fam'/> | 1304 <extra_files type="file" name="RgeneticsData.fam" value="test6_out.fam"/> |
1286 </output_collection> | 1305 </output> |
1306 <expand macro="log_out_assert"/> | |
1287 <output name='mds' value='plink.mds' compare='sim_size'/> | 1307 <output name='mds' value='plink.mds' compare='sim_size'/> |
1288 <output name='cluster1' value='plink.cluster1' compare='sim_size'/> | 1308 <output name='cluster1' value='plink.cluster1' compare='sim_size'/> |
1289 <output name='cluster2' value='plink.cluster2' compare='sim_size'/> | 1309 <output name='cluster2' value='plink.cluster2' compare='sim_size'/> |
1290 <output name='cluster3' value='plink.cluster3' compare='sim_size'/> | 1310 <output name='cluster3' value='plink.cluster3' compare='sim_size'/> |
1291 <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/> | 1311 <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/> |
1292 </test> | 1312 </test> |
1293 | 1313 |
1294 <test expect_num_outputs='8'> | 1314 <test expect_num_outputs='5'> |
1295 <section name='inputs'> | 1315 <section name='inputs'> |
1296 <conditional name='inputs'> | 1316 <conditional name='inputs'> |
1297 <param name='filetype' value='bfile'/> | 1317 <param name='filetype' value='bfile'/> |
1298 <param name='bed' value='plink.bed'/> | 1318 <param name='bed' value='' ftype="pbed"> |
1299 <param name='bim' value='plink.bim'/> | 1319 <composite_data value="plink.bim"/> |
1300 <param name='fam' value='plink.fam'/> | 1320 <composite_data value="plink.bed"/> |
1321 <composite_data value="plink.fam"/> | |
1322 </param> | |
1301 </conditional> | 1323 </conditional> |
1302 </section> | 1324 </section> |
1303 <conditional name='functions'> | 1325 <conditional name='functions'> |
1304 <param name='func' value='association'/> | 1326 <param name='func' value='association'/> |
1305 <conditional name='assoc'> | 1327 <conditional name='assoc'> |
1326 <param name='beta' value='beta'/> | 1348 <param name='beta' value='beta'/> |
1327 <param name='intercept' value='intercept'/> | 1349 <param name='intercept' value='intercept'/> |
1328 </conditional> | 1350 </conditional> |
1329 <param name='lambda' value='1.0'/> | 1351 <param name='lambda' value='1.0'/> |
1330 </conditional> | 1352 </conditional> |
1331 <output_collection name='plink_out' type='list'> | 1353 <output name="plink_out"> |
1332 <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/> | 1354 <extra_files type="file" name="RgeneticsData.bed" value="out.assoc.bed" compare='sim_size'/> |
1333 <element name='plink_bim' file='out.assoc.bim'/> | 1355 <extra_files type="file" name="RgeneticsData.bim" value="out.assoc.bim"/> |
1334 <element name='plink_fam' file='out.assoc.fam'/> | 1356 <extra_files type="file" name="RgeneticsData.fam" value="out.assoc.fam"/> |
1335 </output_collection> | 1357 </output> |
1358 <expand macro="log_out_assert"/> | |
1336 <output_collection name='assoc_outfiles' type='list' count='2'> | 1359 <output_collection name='assoc_outfiles' type='list' count='2'> |
1337 <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/> | 1360 <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/> |
1338 <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/> | 1361 <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/> |
1339 </output_collection> | 1362 </output_collection> |
1340 <output_collection name='adjust_outfiles' type='list' count='1'> | 1363 <output_collection name='adjust_outfiles' type='list' count='1'> |
1345 <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/> | 1368 <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/> |
1346 <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/> | 1369 <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/> |
1347 </output_collection> | 1370 </output_collection> |
1348 </test> | 1371 </test> |
1349 | 1372 |
1350 <test expect_num_outputs='6'> | 1373 <test expect_num_outputs='3'> |
1351 <section name='inputs'> | 1374 <section name='inputs'> |
1352 <conditional name='inputs'> | 1375 <conditional name='inputs'> |
1353 <param name='filetype' value='bfile'/> | 1376 <param name='filetype' value='bfile'/> |
1354 <param name='bed' value='plink.bed'/> | 1377 <param name='bed' value='' ftype="pbed"> |
1355 <param name='bim' value='plink.bim'/> | 1378 <composite_data value="plink.bim"/> |
1356 <param name='fam' value='plink.fam'/> | 1379 <composite_data value="plink.bed"/> |
1380 <composite_data value="plink.fam"/> | |
1381 </param> | |
1357 </conditional> | 1382 </conditional> |
1358 </section> | 1383 </section> |
1359 <conditional name='functions'> | 1384 <conditional name='functions'> |
1360 <param name='func' value='ibd'/> | 1385 <param name='func' value='ibd'/> |
1361 <conditional name='genome'> | 1386 <conditional name='genome'> |
1363 <param name='min' value='0.1'/> | 1388 <param name='min' value='0.1'/> |
1364 <param name='max' value='0.9'/> | 1389 <param name='max' value='0.9'/> |
1365 <param name='modifiers' value='full,unbounded,nudge'/> | 1390 <param name='modifiers' value='full,unbounded,nudge'/> |
1366 </conditional> | 1391 </conditional> |
1367 </conditional> | 1392 </conditional> |
1393 <expand macro="log_out_assert"/> | |
1368 <output name='genome' file='out.genome'/> | 1394 <output name='genome' file='out.genome'/> |
1369 </test> | 1395 </test> |
1370 </tests> | 1396 </tests> |
1371 <help><![CDATA[ | 1397 <help><![CDATA[ |
1372 PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | 1398 PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |